2XEA | pdb_00002xea

4.6 ANGSTROM CRYO-EM RECONSTRUCTION OF TOBACCO MOSAIC VIRUS FROM IMAGES RECORDED AT 300 KEV ON A 4KX4K CCD CAMERA


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XEA 
Sample
TOBACCO MOSAIC VIRUS
Specimen Preparation
Sample Aggregation StateFILAMENT
Vitrification InstrumentHOMEMADE PLUNGER
Cryogen NameETHANE
Sample Vitrification DetailsLIQUID ETHANE
3D Reconstruction
Reconstruction MethodHELICAL
Number of Particles5300
Reported Resolution (Å)4.6
Resolution Method
Other DetailsBPRP WAS USED TO RECONSTRUCT THE 3D VOLUME THE PDB 2OM3 WAS DOCKED INTO THE CRYO-EM DENSITY USING CHIMERA. SOME SIDE CHAIN RESIDUES AND THE INNER LOOP ...BPRP WAS USED TO RECONSTRUCT THE 3D VOLUME THE PDB 2OM3 WAS DOCKED INTO THE CRYO-EM DENSITY USING CHIMERA. SOME SIDE CHAIN RESIDUES AND THE INNER LOOP OF THE CP WERE REMODELLED USING COOT. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1730
Refinement Type
Symmetry TypeHELICAL
Map-Model Fitting and Refinement
Id1 (2XEA)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement TargetCross-correlation coefficient
Overall B Value
Fitting Procedure
DetailsMETHOD--RIGID BODY, REAL SPACE REFINEMENT PROTOCOL--CRYO-EM
Data Acquisition
Detector TypeGATAN ULTRASCAN 4000 (4k x 4k)
Electron Dose (electrons/Å**2)25
Imaging Experiment1
Date of Experiment2009-02-01
Temperature (Kelvin)78
Microscope ModelFEI TECNAI F30
Minimum Defocus (nm)900
Maximum Defocus (nm)3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.3
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification90000
Calibrated Magnification121000
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
MODEL FITTINGCoot
MODEL FITTINGUCSF Chimera
RECONSTRUCTIONIMAGIC
RECONSTRUCTIONSPIDER
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
EACH PARTICLE WAS FULLY CTF CORRECTED